Hi all,
I am trying to change a water molecule near a metal site to include a vdw
term of the hydrogens if I just keep it as a tip3 the hydrogens get to
close to the metal site.
When I look in the parameter file (parm94.dat ) I see that there is a flag
HW OW 0000. 0000. 4. flag for fast
water
which is for TIP3. If I just rename the residue type and change the charge
according to some QM computation I get an error that this flags is not
specified for my new residue type.
If I have copied the TIP3 parameters and change the parameters
HW -> H
and
OW -> OH
would that flag be ignored or is it somewhere in the library file for TIP3
- solvents.lib:
!entry.TP3.unit.atoms table str name str type int typex int resx int
flags int seq int e
lmnt dbl chg
"O" "OW" 0 1 131072 1 8 -0.834000
"H1" "HW" 0 1 131072 2 1 0.417000
"H2" "HW" 0 1 131072 3 1 0.417000
!entry.TP3.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"O" "OW" 0 -1 0.0
"H1" "HW" 0 -1 0.0
"H2" "HW" 0 -1 0.0
!entry.TP3.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.TP3.unit.childsequence single int
2
!entry.TP3.unit.connect array int
0
0
!entry.TP3.unit.connectivity table int atom1x int atom2x int flags
2 1 1
2 3 1
3 1 1
!entry.TP3.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
!entry.TP3.unit.name single str
"TP3"
!entry.TP3.unit.positions table dbl x dbl y dbl z
0.0 0.0 0.0
0.957200 0.0 0.0
-0.239988 0.926627 0.0
!entry.TP3.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
0 0 0 0 0 0
!entry.TP3.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"WAT" 1 4 1 "w" 1
!entry.TP3.unit.residuesPdbSequenceNumber array int
0
!entry.TP3.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.TP3.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
I have add all the bonds to new.frcmod from TIP3 but still I have this
issue.
Thanks for any suggestions to correct this behavior.
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Received on Sun Feb 01 2015 - 11:30:02 PST
